I personally have not owned hard shell units but have spent time wheeling with people that do and have paid a lot of attention to them because I was always interested. So here is what my experience has earned me:
- Ease of deployment and pack-up (wet and dry)
Hard shell: very easy to open and pack. Snow or rain do not offer an issue in most cases. Most designs open in under a minute and close in a bit over that (have to fold material in so it doesn't pinch.
Fold up design: easy to open but requires more work. A bit of a pain to fold when raining or snowing. About two minutes to open (once you're used to it and if you don't have other accessories to setup) and about 4 minutes to close (after practice). The big side effect is having to go around it several times to tuck all the material in and then put the outside cover over it and secure it.
- Aerodynamics (fuel economy, noise).
Both are large boxes mounted on your roof with a gap under it acting like a very crappy spoiler. The hard shell ones are usually more aerodynamically designed but it's not like you're driving a race car. When they are on the roof, they all offer drag and resistance. If you have a pickup you can mount it at the same height as the roof and that's about the only way of reducing the drag.
- Water resistance (during wind or heavy vertical downpour)
Hard shell: The biggest negative of the hard shell design is their lack of awnings over windows and entry way. When it rains and you open it you're letting water in. Otherwise they work great.
Fold up: most fold up designs have covers over windows and door and give additional awnings that allow for dry entrance. I've never had mine leak even in really bad weather. When folded up wet the water has never seeped into the inside and my mattress and sleeping bag remained dry.
Both: the material should be regularly treated with waterproofing sprays meant for that material. Of course, when possible, dry after use to limit the chances of mold. When not using between trips, take the mattress out and store separately to limit the chance of mold.
- Wind resistance (noise and side wall stability) - important in the desert.
Fold up: fairly noisy during extremely windy weather due to the amount of material and different layers.
Hard shell: no clue, but they appear to be very sturdy and less noisy.
- Condensation and ventilation.
Fold up: a little, especially on cold nights, the factory little vents up top are almost useless, usually I crack a window a 1/4 way down and it works. A good option is to have a little space heater (coleman style works) and fire it up right before you plan getting up. Gets rid of condensation and heats up the tent too.
Hard shell: no clue.
- Weight and effect on center of gravity ( off chamber).
Fold up: around 110lbs +/-
hard shell: most designs are 120lb to 180lbs or more depending on model.
- Fold out style (gain shelter) vs. pop up hard-shells (no shelter).
For my needs the fold out style is better mainly because it provides the additional shelter and ability to leave stuff outside, hanging below the awning and still be dry (rain coat, boots, etc). It is more complicated to close up especially if raining or snowing and it is annoying to have to go around a couple times to be able to close it up. You do have to do something similar with the hard shell ones too and tuck in all the material but it is a lot quicker.
When designing the setup make sure to have good access all around your tent and can reach up to it to be able to tuck everything in with ease.
On a side note, the cheaper roof top tents that fold out (and the old ARB tents) were designed with a small "flaw". The awning over the stairs was designed to stand out more but was unsupported in the middle (first pic) which causes for rainwater and snow to collect up there and weigh it down. Basically creating a nice, heavy pool right in the middle. The new design (second pic) gives less room but doesn't collect any water. As far as I know only ARB is doing this, the rest of the guys still haven't figured it out.
There is always the price issue as well. The hard shell units are a lot more expensive.
There are some new options out there these days though:
http://www.cascadiatents.com/Mt-Thielsen.htm?m=87&s=615&&id=162
http://www.bigfoottents.com/Hard-Shell-Roof-Top-Tent-_p_9.html
that ones looks to have finally done an awning over the entrance.